"If it had been done earlier, it would've been better for Microsoft," Cook said during a second-quarter earnings call on Wednesday.

In the time Microsoft lost, Apple's iWork and other productivity suites filled the gap. But Microsoft's Office is critical software for the iPad, especially in enterprises, and customers are responding well, Cook said.

"I do see that Office is a very key franchise in the enterprise," Cook said. "I wholeheartedly welcome Microsoft to the App Store."

It was a moment of rare Apple praise for Microsoft, which is going through a transition period after Satya Nadella became the company's new CEO in February. Right after this appointment, Nadella outlined a "mobile first, cloud first" strategy revolving around a cohesive set of applications in the cloud that can work across devices.

During the second fiscal quarter ended March 29, iPad shipments totaled 16.35 million units, falling from 19.48 million units in the same quarter the previous year. But the company remains upbeat on the iPad, with new products in the pipeline, Cook said.

"That doesn't mean every quarter ... [there's] going to be a number that everyone's thrilled with," Cook said.

Cook also said that iPad shipments will overtake PCs in the coming years. Apple has sold 210 million iPads since the tablet's launch in 2010. That's twice as many units as the iPhone sold in its first four years, and seven times the figure for iPods.